So before you go cutting out your D3 harnesses, know that you don't have to. The plugs as well as the wire locations on those plugs are exactly the same for both units. All you have to do is unplug your D3, move the mute wire to the new bypass pin location, and plug the F90BT (or F900BT) in using the D3 harnesses.
I found this out only AFTER completely removing both harnesses from my car. I heard a few sources stating that the harnesses were different... So I just went ahead and started cutting it out and only discovered this after the fact. But now I know 100% that both of these units have the same wiring harnesses. And looking over Pioneer's parts site, it lists both the power and RCA harnesses of the F90BT and F900BT as the same exact parts, so it's a good bet to sat that they are the same as well. But Pioneer lists the F700BT's harnesses with different part numbers, so I'd assume they are different, and not interchangeable with the D3 harnesses.
Also... the antenna wire plug is different, but it also looks like you can just slip off the green cable end from the F90BT's antenna and use it to replace the cable end from the old D3 antenna and it should work with the F90BT just fine.